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One month prior to Samus' arrival on Aether, Squad Bravo was sent to track a Space Pirate Flagship, heading for the planet Aether, in the Dasha Reigon. Squad Bravo soon caught up to the Flagship, but the Marine's ship, the G.F.S. Tyr, was damaged, due to a severe storm, (part of the rapid unstability and dimensional flux which Aether was undergoing at the time) and they lost track of the flagship. Fortunately, they landed safely in the Temple Grounds. The G.F.S. Tyr was suffering heavy damage, and was virtually useless, other than for protection from the weather, and other natural threats. However, Squad Bravo had started to work on the ship, splitting into two groups, one for repairs on the ship, one for setting up Ops Base. According to Exeter's final report, "Each Station was doing fine, no problems. Until they appeared." All of a sudden, a Dark Portal appeared, and a large swarm of Dark Splinters emerged. There was a long fight between Squad Bravo and the Dark Splinters. In the end, however, most of the Troopers were killed, while the survivors were later possessed by several Ing and turned into Dark Troopers.

The Missile Trooper was turned into a Dark Missile Trooper and became a miniboss. However, the only upgrade is a Missile Expansion, but one that curiously is identical to the Missile Launcher, suggesting it is in fact the Launcher stolen from Samus by the Ing.

One month later, Samus Aran was sent on a search-and-rescue mission by the Galactic Federation. She was too late; all the Troopers were either dead or possessed. Samus was still able to gather the Trooper Logs, and learn what happened. She found Exeter's final report, which gave a full video of what happened. In Echoes, Squad Bravo is the cause of Samus' arrival on Aether. Upon discovering the deceased squadron, Samus journeys to discover their attackers' identity, eventually leading her to U-Mos and the story of the Luminoth-Ing war.

It is unknown what happened to the corpses of the Squad after Dark Aether collapsed, particularly those possessed, but it is likely the possessed Troopers became exorcised. Being that the Federation traveled to Aether later on and discovered Phazon there, it is likely that they retrieved all trooper bodies and brought them somewhere for an honored memorial service.